mergeBed command not found

[cmccabe]

I am running bedtools 2.17.0 and using the mergeBed command I get an error that says comand not found

 mergeBed -i hgTables.bed > merged.bed

The mergeBed folder is in the srcdirectory and has Makefile, mergeBed.cpp, mergeBed.h, mergeMain.cpp in it. Thank you.

[dpryan]

It's not in your PATH then. It's simplest to keep executables in ~/bin or somewhere like that and then just copy things there after you compile them.

[cmccabe]

So are you saying to put the hgTables.bed in the bin? Where is the executable for bedtools, I though that was the main folder. Thank you.

[dpryan]

No, put the executables in a folder in your path and keep the bed files where ever they currently are. When you type a command, the list of folders in the $PATH are traversed until the executable is found. Since the mergeBed executable isn't in one of those, you get the error. So, either move it to one of those or change the variable (how to do this depends on your shell, which is likely bash).

[cmccabe]

So I put the hgTables.bed in the /home/dnascope/bedtools_2.17.0/bin and changed the directory to there. I can see the mergebed executable there, but when I run the command

 mergeBed -i hgTables.bed > merge.bed

the mergeBed command is not found. Thank you for your help.

I also tried, /home/dnascope/bedtools_2.17.0/bin and changed the directory to there andleaving the hgTables in the Bedtools-2.17-0 folder outside the bin folder with the same result.

[dpryan]

As I said, /home/dnascope/bedtools_2.17.0/bin isn't in your PATH. Very few systems will looks for executables in your current directory (it's good way to shoot yourself in the foot). You could just:

./mergeBed -i hgTables.bed > merge.bed

since you're already in the same directory. "./" is just short-hand for "the directory I'm in". If you give the path to an executable when you issue a command, then the system will alternatively just look there (obviously, this requires more typing, which is why moving executables to a directory in the $PATH is normally done.

[cmccabe]

Thanks that worked. Out of curiosity what is the $PATH of bedtools or is there a way to find it in ubuntu? Thanks

[dpryan]

$PATH is a variable used by your shell. The actual path of bedtools is where ever you put it (you can use the "find" function should you ever forget). You'll want to get a book on using unix/linux.